Building real friendships

I've just returned from a GRADschool course in Windermere run by Vitae (and paid for by SGM - THANK YOU!!) which I was warned might change my life, and has indeed done so.

Aside from boosting my confidence no end and giving me some very firm nudges in the right direction career-wise, it has reaffirmed my desire to live a life that I find fulfilling, nourishing and challenging. It also highlighted to me that I am a very people-oriented person. I just love caring for and bringing the best out of people, getting to know them, supervising projects so that everyone does their bit (it turns out I'm a Belbin co-ordinator) and making sure everyone knows how vital they were in getting stuff done.

So whilst evaluating my time there, one thread that stood out was my pain at not keeping in touch with my friends better. Every time I miss a birthday or a marriage or a birth I cringe. How do I not know my friend's addresses, mobile numbers... birthdays?!

Unfortunately a large part of the answer lies in Facebook.

It has become my crutch. Where I once had an address book I now just send people messages online. I decided this won't do, so tonight I culled about 100 people off my friend list. I began with people I haven't spoken to in the last year - which was a surprising number; most of these I haven't really spoken to since I joined Facebook back in 2006. Once the ball was rolling, it was easier to remove people who I am awkwardly friends with through other friends, people I went to school with, and people who generally just make me feel shite about myself. Now I'm down to 146 friends, which still seems an awful lot.

 




Since I became friends with my mum, my aunties and my vicar, I have to say I've been putting a lot less stuff on my page (!), but the weird thing is that online etiquette has changed in recent years, and I've become accepting of some seriously detrimental things. Since when was it ok for people I barely know to write upsetting things in my personal space? Since when do I need to share my personal details with people I haven't really spoken to in 15 years, or with friends of friends? It's bizarre, and I can understand how Facebook has been found to have profound mental implications. I know far more intimate details about certain conference contacts than I do of some of my work colleagues.

So I've chopped my social sphere down to people I like and want to stay in touch with, which surely is what Facebook should be for. Who knows, I may yet give it all up completely... but for now I'm happy to have a bit more control over who can see my personal stuff, and begin making a proper address book.

Diversity

This article was originally published for Cambio Ltd. on 14-11-2012. Access it here.

In my original project description there is a very innocuous sentence that reads “rhizobia diversity will be assessed by PCR fingerprinting with REP/ERIC/BOX PCR”.

The problem is, it won’t.

Unfortunately, neither will RP01, RP04 or RP05 RAPD primers, or NodA or GyrB primers, as 2 years of tweaks and frustration have shown me. It would seem I’m at a dead end. So with a year to go, 1000 strains and a £2,000 budget I am faced with the dilemma of how to address my project title of “Rhizobia Diversity in Farm Soils”. Hum.

One of the main problems of this is the more I delve into the topic, the more I wonder what ‘diversity’ means. A quick look in my Chambers dictionary yields the definition:

n diverˈsity state of being diverse; difference; dissimilarity; variety.

But how much difference? How much dissimilarity? How much variety?

I’m beginning to see why I will be a doctor of philosophy…

My original hope was to use banding patterns to identify my strains. My NodA assay very reliably gives me two very different banding patterns for the two bacteria I work with: Rhizobium leguminosarum bv. trifolii and Sinorhizobium meliloti. But it doesn’t give me any finer resolution, and I can already identify with some reliability to the species level because of the plant I’ve isolated them from in the first place. And I must say looking at a plant is a much quicker way of discerning that level of diversity!

So discernment to a species level is pretty easy when you’re coming at it from the direction I am. If it comes off an alfalfa plant, chances are it’s S. meliloti. No need to spend a week showing that molecularly. But my project is aimed at discerning more subtle differences that might have been responsible for crop failures in a previous project: perhaps changes in a gene that affects nodulation ability under low pH, or desiccation, or Ca deficiency. Or something that improves N-fixation ability. Or, or, or… something!

So how do I find that difference?

There are currently 92 species of ‘true’ rhizobia in 12 genera, though it sometimes seems that these classifications change on a bi-weekly basis. I think I’m right in saying that they’re based on 16S rRNA profiles: differences in sections of housekeeping genes that are similar, but whose differences merit their classification as a separate species.

This week I had my first lesson in metagenomics and phylogeny, a combination of brain-crunching pain and excitement at delving into the private lives of my bacteria. Using the 16S rRNA sequence data for 4 wild-type strains of S. meliloti, including its sister strain S. medicae, I crunched them in BioEdit and found… very little difference.

16S is clearly not the gene I will be using for this method.

There are other options though, and with the age of next-generation sequencing upon us it is much easier to analyse diversity at a very fine level using this method: it is clearly the way forward. The problem is the cost. I have almost 1000 strains, far more than I can afford to sequence. My alternative is RFLP, which is cheaper but a nightmare to analyse for that many samples, and won’t give me such fine detail. So I am left with a dilemma that must be familiar to a lot of university-based researchers: how do I squeeze the best value out of my funding? How can I get some original, publishable, rigorous results? At this point I’m considering paying for the sequencing myself!

Free stuff, w00p!

I read in a Lawrence D. Hills book that "there is no honour amongst gardeners" and I'm inclined to agree. Over the past year or two I have become used to finding random vegetables amongst my plants, where people have clearly flung their unwanted stuff. Quite what is wrong with their compost heaps I don't know, but the bizarre thing is that most of the time it seems fine to me. Free veg, great!

Today I went to our Reading allotment where I am continuing to strip it down as we now have *the new allotment*. As it's autumn time it's time to take the beans down - and on arrival at the beans I discovered a whole pile of someone else's bean plants (which just seems plain cheeky).

The thing was, amongst the 'waste' there were absolutely loads of beans. It was here that I decided once and for all that people in this country are mad. We just have too much cheap food - otherwise why would you throw away perfectly good protein in the form of beans?

Personally I will be storing them to grow next year. There's all sorts of runner bean varieties and a few borlottis for good measure.  But there may just be too many to grow, in which case, that's some free food.

Thank you wasteful person!